Joss-reviews: [REVIEW]: starfish: scalable pipelines for image-based transcriptomics

[whedon]

Submitting author: @neuromusic (Justin Kiggins)
Repository: https://github.com/spacetx/starfish
Version: v0.2.1
Editor: @csoneson
Reviewer: @giovp, @shazanfar, @vals
Archive: Pending

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Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@giovp & @shazanfar & @vals, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @csoneson know.

✨ Please try and complete your review in the next six weeks ✨

Review checklist for @giovp

Conflict of interest

• [x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@neuromusic) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [ ] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @shazanfar

Conflict of interest

• [x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@neuromusic) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [ ] Functionality: Have the functional claims of the software been confirmed?
• [ ] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• [ ] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [ ] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [ ] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @vals

Conflict of interest

• [x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@neuromusic) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [ ] Functionality: Have the functional claims of the software been confirmed?
• [x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [ ] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [ ] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @giovp, @shazanfar, @vals it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

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[whedon]

Reference check summary:

OK DOIs

- 10.1016/j.cell.2019.05.031 is OK
- 10.1016/j.cell.2018.05.035 is OK
- 10.1038/nmeth.3252 is OK
- 10.1186/s13059-017-1382-0 is OK
- 10.1073/pnas.1612826113 is OK
- 10.1038/nmeth.2563 is OK
- 10.1038/s41592-018-0175-z is OK
- 10.1093/nar/gkx1206 is OK
- 10.1126/science.aat5691 is OK
- 10.5281/zenodo.59499 is OK
- 10.7717/peerj.453 is OK
- 10.5281/zenodo.3710410 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[csoneson]

👋 @giovp, @shazanfar, @vals - thanks for accepting to review this submission! This is where the review will take place. In the post above you can find your respective checklists, and some additional information and instructions. Don't hesitate to ping me if you have any questions!

[csoneson]

@whedon re-invite @vals as reviewer

[whedon]

OK, the reviewer has been re-invited.

@vals please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[giovp]

To me, first round of review finished, would like to see spacetx/starfish#1899 addressed, in order to explore results.

[vals]

First round finished from my end as well. I would like all my issues addressed. But most importantly from my end there should be versions of the practical examples that can be read without running the notebooks ( https://github.com/spacetx/starfish/issues/1904 ). Even when napari is used, the authors could make versions with screenshots. There is a lot of documentation about all the functionality, but without examples it is hard to get an understanding what the different functionality does.

[csoneson]

Thanks @giovp and @vals for your reviews! @shazanfar - could you give a quick update on the status on your side? Thanks!

[shazanfar]

Thanks for your patience @csoneson ! I've now completed the first round. I agree with @giovp and @vals comments regarding example data and including output in the tutorials. I've also requested amendments & clarification to do with scope + target audience, which I think would make the documentation more easily accessible for users. Thanks again! Cheers, Shila

[csoneson]

Thanks @shazanfar!
@neuromusic - looks like you got some good comments from the reviewers (and that you already started working on some of them 😃). Let me know if you have any questions, and when you are ready for the reviewers to take another look. Thanks!

[neuromusic]

Thanks all! @mattcai and I have started addressing a few of your comments and issues and we will follow up on the rest in the coming weeks.

[neuromusic]

Quick question: How would you prefer we handle closing issues when we feel like we've addressed them? Should we close them or is it best to wait for our reviewers to close them when they are happy?

[csoneson]

@neuromusic - if you are confident that the issue has been addressed I think you can close the issue, with a comment explaining the changes that were made. You can also consult with the reviewer first, in case additional clarifications are needed.

[csoneson]

👋 @neuromusic - just wanted to check in quickly to see how things are going. Let us know if there are any questions.

[csoneson]

ping @neuromusic

👋 @neuromusic - just wanted to check in quickly to see how things are going. Let us know if there are any questions.

[neuromusic]

Thanks for the ping :D I'll follow up on the remaining issues shortly.

[csoneson]

👋 @neuromusic - just checking in here. Do you have an ETA for the remaining fixes? Of course, let us know if there are any questions.

[neuromusic]

sigh. time flies. I'll take care of the remaining issues this week.

sorry about the delay :(

[csoneson]

sigh. time flies. I'll take care of the remaining issues this week.

sorry about the delay :(

@neuromusic - any update on this?

[csoneson]

@neuromusic - any update on the remaining issues?

[csoneson]

@neuromusic, please update us on the status of the remaining issues. If you don't have time to work on this now, let us know and we'll pause this submission.

[csoneson]

I will pause this submission for now.
@neuromusic - do you think you will have the time to work on the remaining issues within the next month? If not, in order to respect the reviewers' time and availability committment, I will propose to close (reject) this submission, and invite a resubmission at a later point in time.

[neuromusic]

I'm sorry for my poor communication over the past month. I've been up against some deadlines, but I expect to be able to address the remaining issues within the next 3 weeks.

[csoneson]

Thanks @neuromusic!

[csoneson]

👋 @neuromusic - just checking in that we're still on track to have these issues addressed within the next week.

[csoneson]

👋 @neuromusic - just checking in that we're still on track to have these issues addressed within the next week.

ping @neuromusic - could you please give us an update on your progress?

[neuromusic]

you can expect a response to the outstanding issues tomorrow :D

[neuromusic]

Thank you for your patience, @csoneson and all.

I've made changes to the documentation and manuscript to satisfy the outstanding issues from @vals and @shazanfar in PR #1913, except for the request for rendered examples in starfish#1904, which I've addressed in a comment on that issue.

As soon as the tests pass and my colleague @mattcai reviews the PR, these changes will be live in the manuscript and documentation.

[csoneson]

Thanks @neuromusic. I have removed the paused label. Once the changes are merged you can ask whedon to re-render the manuscript: @whedon generate pdf, and @giovp, @shazanfar, @vals can have a look at the revisions.

[neuromusic]

@whedon generate pdf

[whedon]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[neuromusic]

Heads up @csoneson we're going to need to make a couple of tweaks to the Acknowledgements before this is published. We should have them by the end of the week.

[csoneson]

Sure, no problem. The next step now is for the reviewers to have another look at the submission and the changes that you have made, and update their checklists above accordingly if they're happy with the current state.

@giovp, @shazanfar, @vals - this should be ready for another look from you now. Don't hesitate to let me know if there are any questions. Thanks!